Jacques van Helden

30 papers Journal 25Unranked 5

Year	Rank	Type	Title / Venue / Authors
2022	J	`jnl`	RSAT 2022: regulatory sequence analysis tools. Nucleic Acids Res. Walter Santana-Garcia, Jaime Abraham Castro-Mondragón, Mónica Padilla-Gálvez, Nga Thi Thuy Nguyen, Ana Elizondo-Salas, Najla Ksouri, François Gerbes, Denis Thieffry, Pierre Vincens, Bruno Contreras-Moreira, Jacques van Helden, Morgane Thomas-Chollier, Alejandra Medina-Rivera
2018	J	`jnl`	RSAT 2018: regulatory sequence analysis tools 20th anniversary. Nucleic Acids Res. Nga Thi Thuy Nguyen, Bruno Contreras-Moreira, Jaime Abraham Castro-Mondragón, Walter Santana-Garcia, Raul Ossio, Carla Daniela Robles-Espinoza, Mathieu Bahin, Samuel Collombet, Pierre Vincens, Denis Thieffry, Jacques van Helden, Alejandra Medina-Rivera, Morgane Thomas-Chollier
2018	J	`jnl`	Sequanix: a dynamic graphical interface for Snakemake workflows. Bioinform. Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen, Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer
2015	J	`jnl`	RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Res. Alejandra Medina-Rivera, Matthieu Defrance, Olivier Sand, Carl Herrmann, Jaime Abraham Castro-Mondragón, Jeremy Delerce, Sébastien Jaeger, Christophe Blanchet, Pierre Vincens, Christophe Caron, Daniel M. Staines, Bruno Contreras-Moreira, Marie Artufel, Lucie Charbonnier-Khamvongsa, Céline Hernandez, Denis Thieffry, Morgane Thomas-Chollier, Jacques van Helden
2012	—	`conf`	eBiomics - A Website Promoting Good Practices and Specific Methods for using Bioinformatics Resources. BIOINFORMATICS Frédérique Lisacek, Patrick Koks, Pascale Berthault, Grégoire Rossier, Guy Bottu, Jacques van Helden, Jean Sylvestre, Jean-Pierre Kraehenbuhl, Jack A. M. Leunissen
2011	J	`jnl`	Prediction of metabolic pathways from genome-scale metabolic networks. Biosyst. Karoline Faust, Didier Croes, Jacques van Helden
2011	J	`jnl`	RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res. Morgane Thomas-Chollier, Matthieu Defrance, Alejandra Medina-Rivera, Olivier Sand, Carl Herrmann, Denis Thieffry, Jacques van Helden
2010	J	`jnl`	Pathway discovery in metabolic networks by subgraph extraction. Bioinform. Karoline Faust, Pierre Dupont, Jérôme Callut, Jacques van Helden
2009	—	`conf`	Gaussian Graphical Models to Infer Putative Genes Involved in Nitrogen Catabolite Repression in S. cerevisiae. EvoBIO Kevin Kontos, Bruno André, Jacques van Helden, Gianluca Bontempi
2009	J	`jnl`	In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. Bioinform. Karoline Faust, Didier Croes, Jacques van Helden
2009	J	`jnl`	Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. Bioinform. Olivier Sand, Morgane Thomas-Chollier, Jacques van Helden
2009	J	`jnl`	info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. Bioinform. Matthieu Defrance, Jacques van Helden
2008	J	`jnl`	Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinform. Rekin's Janky, Jacques van Helden
2008	J	`jnl`	NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Res. Sylvain Brohée, Karoline Faust, Gipsi Lima-Mendez, Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, Jacques van Helden
2008	J	`jnl`	Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinform. Gipsi Lima-Mendez, Jacques van Helden, Ariane Toussaint, Raphaël Leplae
2008	J	`jnl`	RSAT: regulatory sequence analysis tools. Nucleic Acids Res. Morgane Thomas-Chollier, Olivier Sand, Jean-Valéry Turatsinze, Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohée, Jacques van Helden
2006	J	`jnl`	Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinform. Sylvain Brohée, Jacques van Helden
2005	J	`jnl`	CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res. Ulrich Güldener, Martin Münsterkötter, Gabi Kastenmüller, Normann Strack, Jacques van Helden, Christian Lemer, J. Richelles, Shoshana J. Wodak, J. García-Martínez, José E. Pérez-Ortín, Holger Michael, Andreas Kaps, E. Talla, Bernard Dujon, Bruno André, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, Hans-Werner Mewes
2005	J	`jnl`	Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. Bioinform. Didier Gonze, Sylvie Pinloche, Olivier Gascuel, Jacques van Helden
2005	J	`jnl`	Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res. Didier Croes, Fabian Couche, Shoshana J. Wodak, Jacques van Helden
2004	J	`jnl`	Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinform. Nicolas Simonis, Shoshana J. Wodak, G. N. Cohen, Jacques van Helden
2004	J	`jnl`	Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinform. Jacques van Helden
2003	—	`conf`	An Overview of Data Models for the Analysis of Biochemical Pathways. CMSB Yves Deville, David R. Gilbert, Jacques van Helden, Shoshana J. Wodak
2003	J	`jnl`	An overview of data models for the analysis of biochemical pathways. Briefings Bioinform. Yves Deville, David R. Gilbert, Jacques van Helden, Shoshana J. Wodak
2003	J	`jnl`	Regulatory Sequence Analysis Tools. Nucleic Acids Res. Jacques van Helden
2001	J	`jnl`	Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Inf. Sci. Michael Schroeder, David R. Gilbert, Jacques van Helden, Penny Noy
2001	J	`jnl`	From Molecular Activities and Processes to Biological Function. Briefings Bioinform. Jacques van Helden, Avi Naim, Christian Lemer, Renato Mancuso, Matthew D. Eldridge, Shoshana J. Wodak
2000	—	`conf`	Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data. JOBIM Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Michael Schroeder, Shoshana J. Wodak
1999	—	`conf`	Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. German Conference on Bioinformatics Jacques van Helden, David R. Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew D. Eldridge, Kirill Degtyarenko, Shoshana J. Wodak
1999	J	`jnl`	RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. Heladia Salgado, Alberto Santos-Zavaleta, Ulises Garza-Ramos, Jacques van Helden, Edgar Díaz-Peredo, Julio Collado-Vides